scripts/run_experiments.sh
cd ../models/rf_fingerprint
mkdir -p output
BENCHMARK_SET=moleculeace python evaluate.py output/moleculeace
BENCHMARK_SET=polaris python evaluate.py output/polaris

cd ../chemprop_mpnn
mkdir -p output
BENCHMARK_SET=moleculeace python evaluate.py output/direct_moleculeace
BENCHMARK_SET=polaris python evaluate.py output/direct_polaris
BENCHMARK_SET=moleculeace python evaluate.py output/pretrained_moleculeace chemprop_pretrain_baseline.pt
BENCHMARK_SET=polaris python evaluate.py output/pretrained_polaris chemprop_pretrain_baseline.pt

cd ../descriptor_mlp
mkdir -p output
BENCHMARK_SET=moleculeace python evaluate.py output/direct_moleculeace
BENCHMARK_SET=polaris python evaluate.py output/direct_polaris
BENCHMARK_SET=moleculeace python evaluate.py output/pretrained_1MM_moleculeace e16_n2_h4096_best.pt
BENCHMARK_SET=polaris python evaluate.py output/pretrained_1MM_polaris e16_n2_h4096_best.pt
BENCHMARK_SET=moleculeace python evaluate.py output/pretrained_10MM_moleculeace 10MM_best.pt
BENCHMARK_SET=polaris python evaluate.py output/pretrained_10MM_polaris 10MM_best.pt

cd ../molformer_transformer
mkdir -p output
BENCHMARK_SET=moleculeace python evaluate.py output/moleculeace
BENCHMARK_SET=polaris python evaluate.py output/polaris

cd ../minimol
mkdir -p output
BENCHMARK_SET=moleculeace python evaluate.py output/moleculeace
BENCHMARK_SET=polaris python evaluate.py output/polaris

cd ../rf_mordred
mkdir -p output
BENCHMARK_SET=moleculeace python evaluate.py output/moleculeace
BENCHMARK_SET=polaris python evaluate.py output/polaris

cd ../pca_mlp
mkdir -p output
BENCHMARK_SET=moleculeace python evaluate.py output/direct_moleculeace --gpu --pca-method on-the-fly --explained-variance 0.95
BENCHMARK_SET=polaris python evaluate.py output/direct_polaris --gpu --pca-method on-the-fly --explained-variance 0.95
python fit_pca.py pubchem_1MM.zarr  prefitted_pca_model.pt
BENCHMARK_SET=moleculeace python evaluate.py output/pretrained_moleculeace --gpu --pca-method pretrained --pca-model-path prefitted_pca_model.pt
BENCHMARK_SET=polaris python evaluate.py output/pretrained_polaris --gpu --pca-method pretrained --pca-model-path prefitted_pca_model.pt

cd ../molclr
mkdir -p output
python evaluate_moleculeace.py output/moleculeace
python create_benchmark_csv.py
python train_models_polaris.py output/polaris_training
python evaluate_polaris.py output/polaris_evaluation
